Beacon v2 CBI Tools prepares portable Beacon Friendly Format (BFF) data for Beacon v2. Its command-line interface is called bff-tools. It validates phenotypic and clinical metadata, converts VCF or SNP-array TSV input into BFF genomicVariations, and can generate a standalone browser report.
Beacon v2 CBI Tools is the actively developed continuation of the original beacon2-ri-tools codebase, now developed at CNAG Biomedical Informatics by its original developer.
The two historical image badges preserve the download record of earlier distributions; those images are deprecated for new installations.
Read the documentation for installation options, the quick start, the end-to-end tutorial, CLI reference, annotation resources, and troubleshooting.
python3 -m pip install beacon2-cbi-toolsPython 3.10 through 3.14 is supported. Docker, Apptainer, and source/HPC instructions are available in the installation guide.
Check the installation and run the packaged example without downloading annotation databases:
bff-tools doctor
bff-tools demo
- Follow Beacon v2 developments, including VRS alignment.
- Move to Beacon v3 once the specification is finalized.
If you use these tools in published work, please cite:
Rueda M, Ariosa R. "Beacon v2 Reference Implementation: a toolkit to enable federated sharing of genomic and phenotypic data." Bioinformatics, btac568. https://doi.org/10.1093/bioinformatics/btac568
Written by Manuel Rueda, PhD, at CNAG Biomedical Informatics. Licensed under the GNU General Public License v3.0 or later; see LICENSE.